ShrinkWrap deforms second eye
It's doing exactly what it's being told to do. If you view along the Y axis CTRL-numpad 1 and hit numpad 5 for orthographic view, you'll see the 2 eyes are not centered on the ghost in the direction that shrinkwrap is projecting it.

As you have it, in Project mode, Shrinkwrap projects a mesh into another mesh along a defined axis.
The simplest fix, is to move both eyes to be centered across the centre line of the ghost.

Also, apply your rotation so the direction of projection makes more sense, Negative Y.